There are a plenty of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications involve entities which exist at various anatomical levels of granularity and in order to apply such classifications to the Electronic Health Care Records, one needs to build ontologies which are not only based on the formal principles but also take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a way that inferences drawn upon the ontologies would be helpful in interpreting and inferring on the entities which exist at different anatomical levels of granularity. Our case study is on the colon carcinoma, one of the commonest carcinomas prevalent within the European population.